Transitioning from HDF4 to HDF5

Transitioning from HDF4 to
HDF5
Robert E. McGrath (mcgrath@ncsa.uiuc.edu)
Kent Yang (ymuqun@ncsa.uiuc.edu)
NCSA
University of Illinois, Urbana-Champaign
University of Illinois at Urbana-Champaign

McGrath/Yang 2/27/02

1

HDF

Important Note
•

Both HDF4 and HDF5 are supported by the NCSA
HDF group.

•

We will continue to maintain HDF4, as long as we
are funded to do so.

•

We recommend using HDF5, and that you consider
migrating from HDF4 to HDF5 to take advantage of
the improved features and performance of HDF5.

See: http://hdf.ncsa.uiuc.edu/h4-h5.html


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HDF

Main Points
The transition from HDF4 to HDF5 will
require effort.
NCSA is working to assure that the transition is
as smooth as possible

Two main points in this talk:
•
•

Key technical challenges – 3 basic
necessities
Recent NCSA activities – building tools to
meet these needs


3

HDF

I. Key Technical Challenges
The transition to HDF5 involves several technical
challenges:
•
•
•

Support both HDF4 and HDF5 (and HDF-EOS w/4
and HDF-EOS w/5)
Interoperate HDF4 and HDF5 files and libraries
Convert data from HDF4 to HDF5

We are working to provide tools and advice to make
this as easy as possible.


4

HDF

1. Supporting both HDF4 and HDF5
• Will need to support two file formats,
libraries, documentation, etc. for many
years.
– NCSA is committed to support both HDF4 and
HDF5 as long as NASA needs them.

• Training and documentation, etc.
• Tools, etc. need multiple readers, writers


5

HDF

2. Interoperate HDF4 and HDF5
• Many environments will use older HDF4
and newer HDF5 together (e.g., data from
Terra and Aqua)
– This requires two reader/writers, one for HDF4
and one for HDF5.
– Configuration is more complex
• complex configure/make
• potentially, very large binaries
• For HDF-EOS: four+ libraries


6

HDF

2. Interoperate HDF4 and HDF5
• Given software that uses HDFEOS4, it is
usually not difficult to add HDFEOS5
• Many systems already support netCDF,
GEOTiff, etc., supporting two versions of
HDF-EOS is similar.
• The ‘heconvert’ utility uses both HDFEOS4
and HDFEOS5.


7

HDF

3. Convert data from HDF4 to HDF5
• In some cases, may want to convert data
from HDF4 to HDF5 to work with new
software:
– on-demand, as needed
– wholesale, e.g., whole collections

Our experiments show this is quite feasible.
(See below.)


8

HDF

3. Convert data from HDF4 to HDF5
• In many cases, will want a custom conversion,
e.g., per data product
– to capture specific semantics, e.g., relationships
– to optimize the use of HDF5
– to optimize the conversion, e.g., handle large objects,
deal with missing values or compression, etc.

The NCSA libh4toh5 provides a toolkit to help build
conversion utilities. (See below.)


9

HDF

II. Recent NCSA Activities
•
•

NCSA has been establishing a toolkit to support
transition
Tools for Default Conversion of HDF4 to HDF5
– Specification of default mappings
– h4toh5 utility – convert whole file to HDF5
– libh4toh5 – C library to convert individual objects

See: http://hdf.ncsa.uiuc.edu/h4-h5.html


10

HDF

Default Mapping
• Specification of default mapping of HDF4
and HDF5 concepts and objects
– Conceptual guidance for developers
– Standards to help interoperability
– A general purpose solution, should be
customized for particular uses
http://hdf.ncsa.uiuc.edu/HDF5/doc/ADGuide/H4toH5Mapping.pdf


11

HDF

Data Conversion Software
• h4toh5 utility – conversion of 1 HDF4 file to
HDF5
– Implements the mapping specification
– Model for customized conversion utilities

• Libh4toh5 – Library of conversions for single
objects, groups of objects
– Same mapping and algorithms as h4toh5 utility
– Helps construction of custom conversions

For more info ant to obtain: http://hdf.ncsa.uiuc.edu/h4toh5
Feedback on these is requested!


12

HDF

Two Experiments
• Two Experiments testing conversion of HDF4 to
HDF5 data
– Used sample NASA datasets

• Experiment 1: Covert whole files with h4toh5
utility
– Default conversion of standard HDF
– Didn’t convert HDF-EOS objects

• Experiment 2: convert hybrid HDF-EOS files with
heconvert plus libh4toh5
– Convert HDF-EOS objects and other HDF objects


13

HDF

Conclusions
• Conversion from HDF4 to HDF5 is feasible, even
for whole collections
– Could be done on demand, or whole archives could be
converted

• Custom product-specific conversion utilities are
feasible
– This is not particularly difficult
– Demonstrates the effective use of HDFEOS4 and
HDFEOS5 together


14

HDF

Experiment 1: conversion of
NASA datasets to HDF5
• Tested with HDF4 files from NASA
– Files from DIAL, DAACs

• All files converted successfully
• Conversion was fast
http://hdf.ncsa.uiuc.edu/h4toh5/Experiment/h4toh5exp.html



15

HDF



16

HDF



17

HDF

Conclusions
• For many NASA collections, conversion is
feasible and fast
– Could be done on demand, or whole archives
could be converted



18

HDF

Caveats
• Not a representative sample of NASA data
• This is a default conversion: e.g., the result is not
a valid HDF-EOS5 file
– custom conversion would be desirable

• Files with very large individual objects performed
much worse
– newer products have this characteristic
– conversion utility needs better memory management



19

HDF

Experiment 2: ‘Hybrid’ HDF-EOS
files
• heconvert – utility that converts HDF-EOS4 to
HDF-EOS5
– Converts the HDF-EOS objects:
• Grid, Swath, Point
• StructMetadata.0

• Real EOS data are hybrids: they have other HDF4
objects
– Vdata tables, SDS arrays
– ProductMetadata.0, etc.

• These objects are omitted by heconvert


20

HDF

‘Hybrid’ HDF-EOS files
• Discussed this last year: almost all HDF-EOS
files have standard HDF objects as well as HDFEOS object. See previous talk (Workshop IV):
http://hdf.ncsa.uiuc.edu/h4toh5/ESDIS-sep/mcgrath-transitionissues/index.htm

• Key issues
–
–
–
–

Can convert the EOS objects
libh4toh5 can convert other objects individually
But is not trivial to find the ‘other’ objects
Probably requires custom conversion per data product


21

HDF

Experiment: ‘Hybrid’ HDF-EOS files
• Method: added calls to libh4toh5
– Same conversion of EOS objects
– Finds and converts (at least some) of the nonEOS objects
• all Vdatas, annotations, images, ‘lone’ SDSs

• Data: files from the HDF-EOS Sampler CD
– These files all have non-EOS objects


22

HDF

Results and Observations
• Results: libh4toh5 is a useful toolkit for
constructing conversion tools
– In most cases, all the objects are copied to the HDF5
file
– Negligible overhead

• This is a ‘default’ conversion
– Probably not the desired layout of the HDF5
– Would want to use non-default options to libh4toh5, or
possibly write custom
http://hdf.ncsa.uiuc.edu/h4toh5/Experiment2/heconvert.html


23

HDF

Summary
• HDFEOS4 and HDFEOS5 can be used in the
same program
– Can use existing and future data together

• Conversion of HDF4 to HDF5 is feasible
– Conversion could be ‘on demand’ or for whole
collections

• When conversion is desired, will likely want
product-specific conversion
– This is not particularly difficult
– NCSA’s libh4toh5 provides a good initial toolkit


24

HDF

URLs
• NCSA information page:
http://hdf.ncsa.uiuc.edu/h4-h5/

• Conversion Utility Experiment
http://hdf.ncsa.uiuc.edu/h4toh5/Experiment/h4toh5exp.html

• HE Conversion Experiment
http://hdf.ncsa.uiuc.edu/h4toh5/Experiment2/heconvert.html



25

HDF

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